The invention relates to a self-flame retardant antibacterial aqueous polyester resin and a preparation method thereof. The resin comprises the following components in parts by weight: 6.0-12.0 partsof organic anhydride, 3.0-5.0 parts of carboxylic acid Schiff base, 3.0-8.0 parts of polybasic acid, 6.0-20.0 parts of polyhydric alcohols, 1.2-3.5 parts of 2-chloro-5-bromobenzoic acid, 1.5-3.5 partsof dimethylolpropionic acid, 2.0-5.0 parts of xylene, 2.0-5.0 parts of a neutralizing agent and 45.0-65.0 parts of deionized water. The self-flame retardant antibacterial aqueous polyester resin provided by the invention is good in coloring property, low in viscosity, high in hardness, good in fullness, good in brightness, and the like, is free of external flame retardant or antibacterial agent when an aqueous coating is prepared, is long in flame retardant and antibacterial effect lasting and high in efficiency, and can be applied to inner and outer wall coatings, aqueous industrial coatings, aqueous wood product coatings, and the like.